Soem answers for you:
Am I right in thinking that when you have established your "axes des assemblages" that you use them as references from which to measure your mortise and tenon positions?
Not really. The mortises and tenons are laid out on the timbers, not on the floor drawing, which only shows intersections of principle axes.
(as well as initially to enable you to align your timbers on an imaginary horizontal plane parralel to the drawing surface of the floor plan)?
A vertical plane, plumb over the drawing. You still need to level the timbers to get them parallel to the floor drawing.
Are mortises and tenons generally in the centre of posts or beams?
Yes, but not always.
Am I right in thinking that you should only need to align the timbers once, and that the "picage" stage should be fairly quick.
Oui.
If you have to make say 6 trusses, would you align and picage each one from the same original floor plan, instead of using the first completed truss as a pattern?
Definitely; that's the point. The 1st truss could be wonky.